Spicoli TK

Spicoli TK generates surfaces for molecules and volumes enclosed by these surfaces. Spicoli TK can then apply properties to the surface (hydrogen bonding, polarity/hydrophobicity, charge etc.) Spicoli TK writes out these surfaces attached to the molecule, so the surface and the molecule can be visualized together.

For more detailed information on Spicoli TK, check out the link below:

Documentation
An Example of a result obtained from a combination about modeling toolkits: conformers from Omega TK were overlayed using Shape TK while surfaces and coloring were generated by Spicoli TK.
An Example of a result obtained from a combination about modeling toolkits: conformers from Omega TK were overlayed using Shape TK while surfaces and coloring were generated by Spicoli TK.

Modeling

The Modeling suite of toolkits provides the core functionality underlying OpenEye's defining principle that shape & electrostatics are the two fundamental descriptors determining intermolecular interactions. Many of the toolkits in the Modeling suite are directly associated with specific OpenEye applications and can, therefore be used to create new or extend existing functionality associated with those applications.

  • OEChem TK Core chemistry handling and representation as well as molecule file I/O
  • FastROCS™ TK Real-time shape similarity for virtual screening, lead hopping & shape clustering
  • OEDocking TK Molecular docking and scoring
  • Omega TK Conformer generation
  • Shape TK 3D shape description, optimization, and overlap
  • SiteHopper TK Rapid Comparison of Protein Binding Sites
  • Spicoli TK Surface generation, manipulation, and interrogation
  • Spruce TK Protein preparation and modeling
  • Szybki TK General purpose optimization with MMFF94
  • Szmap TK Understanding water interactions in a binding site
  • Zap TK Calculate Poisson-Boltzmann electrostatic potentials

Cheminformatics

The Cheminformatics suite of toolkits provides the core foundation upon which all the OpenEye applications and remaining toolkits are built.

  • OEChem TK Core chemistry handling and representation as well as molecule file I/O
  • OEDepict TK 2D Molecule rendering and depiction
  • Grapheme™ TK Advanced molecule rendering and report generation
  • GraphSim TK 2D molecular similarity (e.g. fingerprints)
  • Lexichem TK name-to-structure, structure-to-name, foreign language translation
  • MolProp TK Molecular property calculation and filtering
  • Quacpac TK Tautomer enumeration and charge assignment
  • MedChem TK Matched molecular pair analysis, fragmentation utilities, and molecular complexity metrics

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